... Hi
I cannot find any similar posts to this on the forum, so please may I ask if anyone can help me?
I have run differential expression on edgeR. I noted that edgeR has a gene ontology and KEGG pathway analysis function so I used it with the code from the users guide and vignette. I downloaded the ...

... That doesn't work either, all I have is a column of numbers from 1 to 31 (for number of samples) and an empty column next to it that says NA in it.
I do not have sufficient coding knowledge to know how to fix this myself. I am perplexed that the r coding in the WGCNA handbook would be so redundant ...

... Hi
I would be very grateful for some help.
I am trying to use WGCNA to perform network analysis on TCGA RNASeq data.
I am at the Data Input and Cleaning stage, after using clustering to exclude outlying samples I am having difficulty making my clinical trait data to align and match with my RNAS ...

... Thank you.
To date I have been using the raw (aligned) counts from the rsem.genes (non normalised) RNASeqV2 total RNA data files. I had assimilated them from cancer and normal tissue samples to do DE analysis using edgeR... is that ok?
...

... I am not familiar with DESeq2, I have been using edgeR up to now. I have just been reading the manuals and online tutorials and looking at how to input the data. I see it will accept a count matrix such as the one I have in csv format, but that it needs a metadata file. I am really not sure how to m ...

... Hey
I have been analysing some of the RNASeq data from TCGA. I have been using total RNA files from RNASeqV2 on the advice of my supervisor. However there are also other types of RNASeq, including exons, splice junctions and isoforms. I've not been able to find somewhere that explains what you can ...

... Hi
I would like to plot RNASeq data that I have downloaded from TCGA in a PCA plot. I have found some great guides on how to plot the actual data in PCA using r in ggplot2 and such but my main question is what format data should I plot?
I currently have raw counts and RSEM data. Should I input raw ...